| Estimation of ADME properties with substructure pattern recognition J Shen, F Cheng, Y Xu, W Li, Y Tang Journal of chemical information and modeling 50 (6), 1034-1041, 2010 | 342 | 2010 |
| Additive CHARMM force field for naturally occurring modified ribonucleotides Y Xu, K Vanommeslaeghe, A Aleksandrov, AD MacKerell Jr, L Nilsson Journal of computational chemistry 37 (10), 896-912, 2016 | 77 | 2016 |
| Investigation of indazole unbinding pathways in CYP2E1 by molecular dynamics simulations Z Shen, F Cheng, Y Xu, J Fu, W Xiao, J Shen, G Liu, W Li, Y Tang PloS one 7 (3), e33500, 2012 | 49 | 2012 |
| LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures YV Pabon-Martinez, Y Xu, A Villa, KE Lundin, S Geny, CH Nguyen, ... Scientific Reports 7 (1), 11043, 2017 | 37 | 2017 |
| Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima E Morgunova, Y Yin, PK Das, A Jolma, F Zhu, A Popov, Y Xu, L Nilsson, ... Elife 7, e32963, 2018 | 36 | 2018 |
| Computational insights into the different catalytic activities of CYP2A13 and CYP2A6 on NNK Y Xu, Z Shen, J Shen, G Liu, W Li, Y Tang Journal of Molecular Graphics and Modelling 30, 1-9, 2011 | 19 | 2011 |
| Validating the CHARMM36m protein force field with LJ-PME reveals altered hydrogen bonding dynamics under elevated pressures Y Xu, J Huang Communications Chemistry 4 (1), 99, 2021 | 12 | 2021 |
| Structural effects of modified ribonucleotides and magnesium in transfer RNAs Y Xu, AD MacKerell Jr, L Nilsson Bioorganic & medicinal chemistry 24 (20), 4826-4834, 2016 | 11 | 2016 |
| Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields Y Ding, Y Xu, C Qian, J Chen, J Zhu, H Huang, Y Shi, J Huang Journal of computer-aided molecular design 34 (4), 421-435, 2020 | 10 | 2020 |
| The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid Y Xu, A Villa, L Nilsson Journal of Computational Chemistry 38 (15), 1147-1157, 2017 | 10 | 2017 |
| The ability of locked nucleic acid oligonucleotides to pre-structure the double helix: A molecular simulation and binding study Y Xu, O Gissberg, YV Pabon-Martinez, J Wengel, KE Lundin, CIE Smith, ... PLoS One 14 (2), e0211651, 2019 | 8 | 2019 |
| Structural Achievability of an NH–π Interaction between Gln and Phe in a Crystal Structure of a Collagen-like Peptide R Zhang, Y Xu, J Lan, S Fan, J Huang, F Xu Biomolecules 12 (10), 1433, 2022 | 4 | 2022 |
| Visualizing cardiolipin in situ with HKCL-1M, a highly selective and sensitive fluorescent probe W Wang, NK Wong, SL Bok, Y Xu, Y Guo, L Xu, M Zuo, CM St. Croix, ... Journal of the American Chemical Society 145 (20), 11311-11322, 2023 | 3 | 2023 |
| Modeling pK Shift in DNA Triplexes Containing Locked Nucleic Acids YD Hartono, Y Xu, A Karshikoff, L Nilsson, A Villa Journal of Chemical Information and Modeling 58 (4), 773-783, 2018 | 3 | 2018 |
| An Additive Charmm Force Field for Modified Nucleic Acids Y Xu, L Nilsson, AD MacKerrel Biophysical Journal 108 (2), 235a-236a, 2015 | 1 | 2015 |
| Codon recognition on the ribosome-free energy and QM/MM calculations L Nilsson, A Villa, Y Xu, Y Hartono, M Ito EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 46, S206-S206, 2017 | | 2017 |
| Molecular Modeling and Thermodynamics Simulation of Nucleic Acids Y Xu PQDT-Global, 2016 | | 2016 |
Jie ShenAbbVieVerified email at abbvie.com
